TkA06G447190 | RubberDandelionOmics

Gene overview

TkA06G447190

Reference: TK1151 Chr: Chr06 Coordinates: 110495043-110498269 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1956 bp · TkA06G447190|TK1151|cDNA

TAAAAAAAGGCTGCCCTTAACTCAAGTTTCCTTGACCTAAACCAGTCGGCGCTCTCTTCTTCTTCGCACCGTCGTGACTGCCTCTTCTCTCGAACGACTAACCTAAACGCAGTCGGCGGCTCCGCTTCTTGTTTGCACCGTCGCCACTGGCTAGTACAGACGACACAACCACTGCGTAGACATCGATAAAGAAAAACGCTTACAATGGATAAGCTCGAAAAGGCACCAAAAGAGGTTCTGGTGGACATCGTGAAGCTGGC...

CDS

Download CDS FASTA

1479 bp · TkA06G447190|TK1151|CDS

ATGGATAAGCTCGAAAAGGCACCAAAAGAGGTTCTGGTGGACATCGTGAAGCTGGCACAAAAGCGAGAAATGAAAGGCAGTAATGGAGGCTGGAAGGAGTTCTTGACTGTTTACGACAAGAAGGTTGGGGTCAGCTTGAGTGATCCAGCAAGAAGGTCCCCTGAAGCATTGCTTGCTTTCTTGAATACATTCACTAACGTTGATGATTTAAAGTTCTTTGATAAAGTCGCGGAGAAACATTTCAGCAATGAGCATATCGA...

Protein

Download Protein FASTA

492 aa · TkA06G447190|TK1151|PROTEIN

MDKLEKAPKEVLVDIVKLAQKREMKGSNGGWKEFLTVYDKKVGVSLSDPARRSPEALLAFLNTFTNVDDLKFFDKVAEKHFSNEHIEKKTDKLSPEQELVYKTVGHPQYAQSYSFPSYEEGWVTTKERKKAKANRSNEMVAIDCEMVLCEDGTDALVRVCVVDRELKVKLDELVKPDKPIVDYKTNITGVTAKDLEHVTCSLEDIQGSMRKLLSRGTILIGHSLNNDLQVLKIDHSRVIDTSLVFKYWSGSNFRRPSLND...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`TkA06G447190`
TK1151 ID	TkA06G447190
OH-1004 ID	LXL04_022780
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.000
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	TK1151 / GWHBCHF00000000

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA06G447190

Location Chr06:110495043-110498269 (+)

Description Similar to SDN1: Small RNA degrading nuclease 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g67240`	3'-5' exonuclease degrading single-stranded small RNAs.	No verified direct reference in this release
`At3g50100`	3'-5' exonuclease degrading single-stranded small RNAs.	Degradation of microRNAs by a family of exoribonucleases in Arabidopsis.2008 · DOI: 10.1126/science.1163728
`At5g05540`	3'-5' exonuclease degrading single-stranded small RNAs.	No verified direct reference in this release
`At3g50090`	Putative 3'-5' exonuclease degrading single-stranded small RNAs.	No verified direct reference in this release
`At5g25800`	Probable 3'-5' exonuclease degrading single-stranded small RNAs.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_022780 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0010587 miRNA catabolic process Biological Process

GO:0031125 rRNA 3'-end processing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0016592 mediator complex Cellular Component

GO:0000175 3'-5'-RNA exonuclease activity Molecular Function

GO:0003676 nucleic acid binding Molecular Function

GO:0003723 RNA binding Molecular Function

GO:0004527 exonuclease activity Molecular Function

GO:0008408 3'-5' exonuclease activity Molecular Function

GO:0035198 miRNA binding Molecular Function

KEGG gene cross-reference

ath:AT3G50100

ath:AT5G05540

ath:AT5G67240

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.654

Rank 1 · TkA06G447190 · TK1151

Cytoplasm0.327

Rank 2 · TkA06G447190 · TK1151

Mitochondrion0.072

Rank 3 · TkA06G447190 · TK1151

Cell membrane0.055

Rank 4 · TkA06G447190 · TK1151

Endoplasmic reticulum0.034

Rank 5 · TkA06G447190 · TK1151

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF26656DUF821931-134 aa

PF00929RNase_T59-78 aa

PF01612DNA_pol_A_exo1137-147 aa

PF00929RNase_T140-289 aa

PF01612DNA_pol_A_exo1196-273 aa

PF16473Rv2179c-like199-290 aa

PF23204KIF21A_2nd431-480 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G447190	`PF26656`	DUF8219	31	134	0.019	15.7
TkA06G447190	`PF00929`	RNase_T	59	78	2.3e-09	38.7
TkA06G447190	`PF01612`	DNA_pol_A_exo1	137	147	0.00045	20.8
TkA06G447190	`PF00929`	RNase_T	140	289	2.3e-09	38.7
TkA06G447190	`PF01612`	DNA_pol_A_exo1	196	273	0.00045	20.8
TkA06G447190	`PF16473`	Rv2179c-like	199	290	0.1	13.1
TkA06G447190	`PF23204`	KIF21A_2nd	431	480	0.0059	17.5

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q8RXK2`	Arabidopsis thaliana	sp\|Q8RXK2\|SDN3_ARATH Small RNA degrading nuclease 3	49.500%	Swiss-Prot	Medium
`A3KPE8`	Arabidopsis thaliana	sp\|A3KPE8\|SDN1_ARATH Small RNA degrading nuclease 1	52.100%	Swiss-Prot	High
`Q9FFG1`	Arabidopsis thaliana	sp\|Q9FFG1\|SDN2_ARATH Small RNA degrading nuclease 2	47.700%	Swiss-Prot	Medium
`Q9SN09`	Arabidopsis thaliana	sp\|Q9SN09\|SDN4_ARATH Putative small RNA degrading nuclease 4	46.800%	Swiss-Prot	Medium
`Q8L7M4`	Arabidopsis thaliana	sp\|Q8L7M4\|SDN5_ARATH Small RNA degrading nuclease 5	46.400%	Swiss-Prot	Low

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